Virtual Microscope Improvements

[beniroquai]

Some more ideas how we can contribute to smart microscopy by enhancing the Virtual Microscope Manager

Modalities

• Light-sheet
• general 3D stuff

More ideas

• Different Noise models
• Drift of the stage
• Objective Switching
• Different Samples
• Bleaching
• Multiple Channels / Laser behaviours
• exposure time
• add slm
• load images from Remote / ZARR / Server, etc
• OpenSlide / ZARR

Interfaces

• REST API
• Seperated PyPi package
• Dockercontainer -> test it in different environments

CC:
@hinderling
@HannahSHeil
@brunomsaraiva
@jhnnsrs
@henrypinkard
@nornil
@jacopoabramo

[beniroquai]

@HannahSHeil, do you have a stitched stack of a multicolour high-resolution fluorescence sample somewhere by any chance for testing the multi-channel stuff? :)

[beniroquai]

@hinderling, how would you like to control the SLM in your opinion? Creating a REST Endpoint and upload patterns from a remote software? We do that with our SIM setup + raspi. Works !

[HannahSHeil]

@beniroquai , I had a very old (2021) 3-color sample. Are you aware of the file size of a 3 channel, stitched, z-stack? I'll send you the data and you might have to downsample ;)
I just realized now, did you want a time stack?

[beniroquai]

Great idea with the time-axis ... but let's start with 4d first ^^

[beniroquai]

A little update: The microscope is life based on a docker container:
https://imswitch.openuc2.com/imswitch/index.html